THE ECEPP PACKAGE FOR CONFORMATIONAL ANALYSIS OF POLYPEPTIDES
We present here the FCEPPAK (developed in the laboratory of prof. H.A. Scheraga, Cornell University) and ANALYZE packages for the conformational search of polypeptides that is based on the ECEPP/3 force field. The functions of the program include energy calculation and minimization and global confo...
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| Format: | Article |
| Language: | English |
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Gdańsk University of Technology
1999-07-01
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| Series: | TASK Quarterly |
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| Online Access: | https://journal.mostwiedzy.pl/TASKQuarterly/article/view/2403 |
| _version_ | 1818264410145161216 |
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| author | DANIEL R. RIPOLL ADAM LIWO CEZARY CZAPLEWSKI |
| author_facet | DANIEL R. RIPOLL ADAM LIWO CEZARY CZAPLEWSKI |
| author_sort | DANIEL R. RIPOLL |
| collection | DOAJ |
| description |
We present here the FCEPPAK (developed in the laboratory of prof. H.A. Scheraga, Cornell University) and ANALYZE packages for the conformational search of polypeptides that is based on the ECEPP/3 force field. The functions of the program include energy calculation and minimization and global conformational search using the Electrostatically-Driven Monte Carlo (EDMC) method. The search can be constrained using experimental information e.g., the distance constraints from NMR measurements. The sister program, ANALYZE, allows the user to classify the conformations by means of cluster analysis and fit the statistical weights of the conformations to best fit the experimental observables. The package is extensively parallelized, which allows the user to carry out the conformational search even of comparatively large polypeptides in real time.
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| first_indexed | 2024-12-12T19:34:28Z |
| format | Article |
| id | doaj.art-cae3a161be4646deae02c18736191b0d |
| institution | Directory Open Access Journal |
| issn | 1428-6394 |
| language | English |
| last_indexed | 2024-12-12T19:34:28Z |
| publishDate | 1999-07-01 |
| publisher | Gdańsk University of Technology |
| record_format | Article |
| series | TASK Quarterly |
| spelling | doaj.art-cae3a161be4646deae02c18736191b0d2022-12-22T00:14:21ZengGdańsk University of TechnologyTASK Quarterly1428-63941999-07-0133THE ECEPP PACKAGE FOR CONFORMATIONAL ANALYSIS OF POLYPEPTIDESDANIEL R. RIPOLL0ADAM LIWO1CEZARY CZAPLEWSKI2Cornell University, Cornell Theory CenterUniversity of Gdansk, Faculty of ChemistryUniversity of Gdansk, Faculty of Chemistry We present here the FCEPPAK (developed in the laboratory of prof. H.A. Scheraga, Cornell University) and ANALYZE packages for the conformational search of polypeptides that is based on the ECEPP/3 force field. The functions of the program include energy calculation and minimization and global conformational search using the Electrostatically-Driven Monte Carlo (EDMC) method. The search can be constrained using experimental information e.g., the distance constraints from NMR measurements. The sister program, ANALYZE, allows the user to classify the conformations by means of cluster analysis and fit the statistical weights of the conformations to best fit the experimental observables. The package is extensively parallelized, which allows the user to carry out the conformational search even of comparatively large polypeptides in real time. https://journal.mostwiedzy.pl/TASKQuarterly/article/view/2403peptides and proteinsconformational analysisempirical force fieldsglobal optimization |
| spellingShingle | DANIEL R. RIPOLL ADAM LIWO CEZARY CZAPLEWSKI THE ECEPP PACKAGE FOR CONFORMATIONAL ANALYSIS OF POLYPEPTIDES TASK Quarterly peptides and proteins conformational analysis empirical force fields global optimization |
| title | THE ECEPP PACKAGE FOR CONFORMATIONAL ANALYSIS OF POLYPEPTIDES |
| title_full | THE ECEPP PACKAGE FOR CONFORMATIONAL ANALYSIS OF POLYPEPTIDES |
| title_fullStr | THE ECEPP PACKAGE FOR CONFORMATIONAL ANALYSIS OF POLYPEPTIDES |
| title_full_unstemmed | THE ECEPP PACKAGE FOR CONFORMATIONAL ANALYSIS OF POLYPEPTIDES |
| title_short | THE ECEPP PACKAGE FOR CONFORMATIONAL ANALYSIS OF POLYPEPTIDES |
| title_sort | ecepp package for conformational analysis of polypeptides |
| topic | peptides and proteins conformational analysis empirical force fields global optimization |
| url | https://journal.mostwiedzy.pl/TASKQuarterly/article/view/2403 |
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